In the year 2138, virtual reality gaming is booming. Yggdrasil, a popular online game is quietly shut down one day. However, one player named Momonga decides to not log out. Momonga is then transformed into the image of a skeleton as "the most powerful wizard." The world continues to change, with non-player characters (NPCs) beginning to feel emotion. Having no parents, friends, or place in society, this ordinary young man Momonga then strives to take over the new world the game has become.

Living in the shadow of his talented younger sister, Kyousuke Kosaka conducts a normal lifestyle until he accidentally finds out that she hides a secret. In addition to being smart, pretty, and popular; Kirino Kosaka is also an obsessive consumer of anime and eroge (adult computer games). What will Kyousuke do? Will this tear their already rocky relationship apart or bring them closer together?

Bayron City -- a Mega-Float type city in the Pacific Ocean, which doesn't belong to any particular nation. As the mine for Orgonium, a new energy resource, this city is the most noticed in the world right now, and here special cases caused by demons called "D Hazards" has been occurring frequently. Only a handful of people know about the existence of D Hazards. They are handled by PMCs (Private Military Companies). Shu is a young man living in Bayron City who runs such a company, but his company is tiny. On top of that, he cherry-picks his jobs, so he is always in a bind for money. His life, both publicly and privately, is being supported by the beautiful high school girl Kisara who attends a school in Bayron City.

In the beginning, an "orb" is cast unto Earth. "It" can do two things: change into the form of the thing that stimulates "it"; and come back to life after death. "It" morphs from orb to rock, then to wolf, and finally to boy, but roams about like a newborn who knows nothing. As a boy, "it" becomes Fushi. Through encounters with human kindness, Fushi not only gains survival skills, but grows as a "person". But his journey is darkened by the inexplicable and destructive enemy Nokker, as well as cruel partings with the people he loves.